Camelia, the Perl 6 bug

IRC log for #cdk, 2009-01-18

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All times shown according to UTC.

Time Nick Message
07:29 jbrefort joined #cdk
10:08 bag joined #cdk
10:11 edrin1 joined #cdk
11:06 edrin1 joined #cdk
11:46 CIA-14 cdk: egonw * r13903 /cdk/branches/cdk-1.2.x/src/ (3 files in 3 dirs): Added an atom type for a non-octet representation of nitrogen, parent of N.nitro, with two double bonds
11:54 carsten joined #cdk
13:15 CIA-14 cdk: egonw * r13904 /cdk/branches/cdk-1.2.x/src/test/org/openscie​nce/cdk/atomtype/CDKAtomTypeMatcherTest.java: Added extra unit test
13:15 CIA-14 cdk: egonw * r13905 /cdk/branches/cdk-1.2.x/src/test/org/open​science/cdk/smiles/SmilesParserTest.java:
13:15 CIA-14 cdk: Added assertion to highlight a bug in the SmilesParser to disregard the implicit hydrogen count on the positive
13:15 CIA-14 cdk: nitrogen.
13:29 CIA-14 cdk: egonw * r13906 /cdk/branches/cdk-1.2.x/src/test/or​g/openscience/cdk/qsar/descriptors/​molecular/XLogPDescriptorTest.java: Ignore two more tests which fail due to a bug in the SmilesParser
13:30 CIA-14 cdk: egonw * r13907 /cdk/branches/cdk-1.2.x/src/test/or​g/openscience/cdk/qsar/descriptors/​molecular/XLogPDescriptorTest.java: Loosened the error margin to match what has been reported in CDK News 3.1: 1.0 unit, instead of 0.1, which might have worked but can be considered overfitting
13:38 CIA-14 cdk: egonw * r13908 /cdk/branches/cdk-1.2.x/src​/main/org/openscience/cdk/ (debug/DebugAtomParity.java nonotify/NNAtomParity.java): Removed the getBuilder methods that are not part of the IAtomParity interface
15:55 carsten joined #cdk
16:46 edrin joined #cdk
17:02 CIA-14 cdk: egonw * r13909 /cdk/branches/cdk-1.2.x/src/tes​t/org/openscience/cdk/atomtype/ (CDKAtomTypeMatcherTest.java SybylAtomTypeMatcherTest.java): Added unit tests for bug report #2445178
18:59 CIA-14 cdk: egonw * r13910 /cdk/branches/cdk-1.2.x/src/test/org/openscience​/cdk/interfaces/AbstractAdductFormulaTest.java: Fixed abstract unit test class hierarchy: IAdductFormula extends IMolecularFormulaSet, not IMolecularFormula (fixes #2451244)
19:12 CIA-14 cdk: egonw * r13911 /cdk/trunk/src/main/org/openscience/​cdk/similarity/DistanceMoment.java:
19:12 CIA-14 cdk: Applied patch from cdk1.2.x:
19:12 CIA-14 cdk: Cleaned up Javadocs and moved some code to 1.5 idiom
19:12 CIA-14 cdk: git-svn-id:
19:12 CIA-14 cdk: https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/branches/cdk-1.2.x@12563 eb4e18e3-b210-0410-a6ab-dec725e4b171
19:12 CIA-14 cdk: Author: rajarshi <rajarshi@eb4e18e3-b210-0410-a6ab-dec725e4b171>
19:13 CIA-14 cdk: egonw * r13912 /cdk/trunk/.gitignore:
19:13 CIA-14 cdk: Applied patch from cdk1.2.x:
19:13 CIA-14 cdk: Ignore more autogenerated stuff
19:13 CIA-14 cdk: git-svn-id:
19:13 CIA-14 cdk: https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/branches/cdk-1.2.x@12571 eb4e18e3-b210-0410-a6ab-dec725e4b171
19:13 CIA-14 cdk: Author: egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>
19:14 CIA-14 cdk: egonw * r13913 /cdk/trunk/src/main/org/opensci​ence/cdk/io/ReaderFactory.java:
19:14 CIA-14 cdk: Applied patch from cdk1.2.x:
19:14 CIA-14 cdk: If something is already a GzipInputStream, don't test for gzip-ness again; reuse guessFormat
19:14 CIA-14 cdk: git-svn-id:
19:14 CIA-14 cdk: https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/branches/cdk-1.2.x@12580 eb4e18e3-b210-0410-a6ab-dec725e4b171
19:14 CIA-14 cdk: Author: egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>
19:15 CIA-14 cdk: egonw * r13914 /cdk/trunk/src/test/org/openscien​ce/cdk/io/ReaderFactoryTest.java:
19:15 CIA-14 cdk: Applied patch form cdk1.2.x:
19:15 CIA-14 cdk: Workaround for bug #2153298
19:15 CIA-14 cdk: git-svn-id:
19:15 CIA-14 cdk: https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/branches/cdk-1.2.x@12581 eb4e18e3-b210-0410-a6ab-dec725e4b171
19:15 CIA-14 cdk: Author: egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>
19:16 CIA-14 cdk: egonw * r13915 /cdk/trunk/src/test/org/openscien​ce/cdk/io/ChemObjectIOTest.java:
19:16 CIA-14 cdk: Applied patch from cdk1.2.x:
19:16 CIA-14 cdk: Make a general assertion to all readers about the IChemObject's they accept, which should include IChemFile, IMolecule, IChemModel or IReaction
19:16 CIA-14 cdk: egonw * r13916 /cdk/trunk/src/test/org/openscience/cdk/io/ (ChemObjectReaderTest.java SimpleChemObjectReaderTest.java): Added test classes for two more interfaces
19:17 CIA-14 cdk: egonw * r13917 /cdk/trunk/src/test/org/openscien​ce/cdk/io/ChemObjectIOTest.java: Test that for each IChemObject implementation, at least on object is accepted.
19:17 CIA-14 cdk: egonw * r13918 /cdk/trunk/src/test/org/opensci​ence/cdk/io/XYZReaderTest.java: More testing
19:18 CIA-14 cdk: egonw * r13919 /cdk/trunk/src/main/org/opens​cience/cdk/io/XYZReader.java: Added unit test annotation
19:19 CIA-14 cdk: egonw * r13920 /cdk/trunk/src/test/org/openscien​ce/cdk/io/ChemObjectIOTest.java: Added more testing
19:19 CIA-14 cdk: egonw * r13921 /cdk/trunk/src/test/org/openscience/cd​k/io/SimpleChemObjectReaderTest.java: Test reading in all accepted IChemObject's
19:19 CIA-14 cdk: egonw * r13922 /cdk/trunk/src/META-INF/test-io.cdkdepends: The module test-io now tests accepting all common interface implementations, which adds these dependencies
19:20 CIA-14 cdk: egonw * r13923 /cdk/trunk/src/main/org/opens​cience/cdk/io/XYZReader.java: Added missing annotation
19:21 CIA-14 cdk: egonw * r13924 /cdk/trunk/src/main/org/openscience/cdk/io/ (22 files): Fixed a bug present in many readers: it would not accept a subclass if ChemFile (e.g. NNChemFile) even if ChemFile itself was accepted
19:22 CIA-14 cdk: egonw * r13925 /cdk/trunk/src/main/org/openscience/cdk/io/ (10 files): Added missing TestClass annotation
19:25 CIA-14 cdk: egonw * r13926 /cdk/trunk/src/main/org/openscience/cdk/io/ (48 files in 5 dirs): Added testClose annotation
19:28 CIA-14 cdk: egonw * r13927 /cdk/trunk/src/main/org/openscience/cdk/io/ (48 files in 5 dirs): Added missing testAccepts, testSetReader_InputStream and testSetReader_Reader unit test annotation
19:29 CIA-14 cdk: egonw * r13928 /cdk/trunk/src/test/org/openscience/cdk/io/ (MDLV2000ReaderTest.java PCCompoundASNReaderTest.java): Extend SimpleChemObjectReaderTest for more extensive testing
19:30 CIA-14 cdk: egonw * r13929 /cdk/trunk/src/test/org/openscien​ce/cdk/io/ChemObjectIOTest.java:
19:30 CIA-14 cdk: Applied patch from cdk1.2.x/:
19:30 CIA-14 cdk: Make a general assertion to all readers about the IChemObject's they accept, which should include IChemFile, IMolecule, IChemModel or IReaction
19:30 CIA-14 cdk: git-svn-id:
19:30 CIA-14 cdk: https://cdk.svn.sourceforge.net/svnr​oot/cdk/cdk/branches/cdk-1.2.x@12583 eb4e18e3-b210-0410-a6ab-dec725e4b171
19:30 CIA-14 cdk: Author: egonw <egonw@eb4e18e3-b210-0410-a6ab-dec725e4b171>
19:31 CIA-14 cdk: egonw * r13930 /cdk/trunk/work.txt: Some more patches applied
19:55 CIA-14 cdk: egonw * r13931 /cdk/branches/cdk-1.2.x/src/test​/org/openscience/cdk/io/program/ (. GaussianInputWriterTest.java):
19:55 CIA-14 cdk: Added a test class for GaussianInputWriter
19:55 CIA-14 cdk: git-svn-id:
19:55 CIA-14 cdk: https://cdk.svn.sourceforge.ne​t/svnroot/cdk/cdk/trunk@13862 eb4e18e3-b210-0410-a6ab-dec725e4b171
19:55 CIA-14 cdk: (cherry picked from commit 04bda560634f629385e49f030e7ab3940c7c787a)
19:55 CIA-14 cdk: Author: shk3 <shk3@eb4e18e3-b210-0410-a6ab-dec725e4b171>
20:05 CIA-14 cdk: egonw * r13932 /cdk/branches/cdk-1.2.x/src/main/org/openscie​nce/cdk/io/program/GaussianInputWriter.java: Added missing annotation
20:09 CIA-14 cdk: egonw * r13933 /cdk/branches/cdk-1.2.x/src/test/org/openscienc​e/cdk/io/program/GaussianInputWriterTest.java: Fixed test: close writer, so that we are sure the content is flushed. Also a small test change: test string length, instead of being )
23:32 ilbot2 joined #cdk
23:32 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit CDK 1.2.x: 15112, 130 fails + 42 errors (1.14%) | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk | CDK News paper online on pharmacophores: http://www.cdknews.org/ | CDK News Feed: http://beta.friendfeed.com/ro​oms/chemistry-development-kit

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